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FLARE: Fast Learning of Atomistic Rare Events
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FLARE: Fast Learning of Atomistic Rare Events
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Contents
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Installation
Requirements
Installation using pip
Manual Installation with Git
Acceleration with multiprocessing and MKL
Environment variables (optional)
Tutorials
Prepare your data
VASP data
Data from Quantum Espresso, LAMMPS, etc.
Try building GP from data
Training a Gaussian Process from an AIMD Run
Roadmap Figure
Step 1: Setting up a Gaussian Process Object
Step 2 (Optional): Extracting the Frames from a previous AIMD Run
Step 3: Training your Gaussian Process
Pre-Training arguments
On-the-fly aluminum potential
Step 1: Set up a GP Model
Step 2: Set up DFT Calculator
Step 3: Set up OTF MD Training Engine
Step 4: Launch the OTF Training
On-the-fly training using ASE
Step 1: Set up supercell with ASE
Step 2: Set up FLARE calculator
Optional
Step 3: Set up DFT calculator
Optional: alternatively, set up Quantum Espresso calculator
Step 4: Set up On-The-Fly MD engine
After Training
Parse OTF log file
Construct GP model from log file
Map the GP force field & Dump LAMMPS coefficient file
Run LAMMPS with MGP pair style
Compile LAMMPS with MGP Pair Style
MPI
Compiling
Running
MPI+OpenMP through Kokkos
Compiling
Running
MPI+CUDA through Kokkos
Compiling
Running
Notes on Newton (only relevant with Kokkos)
Code Documentation
Gaussian Process Force Fields
Structures
Python methods
Atomic Environments
Kernels
Single-element Kernels
Multi-element Kernels (simple)
Multi-element Kernels (Separate Parameters)
Cutoff Functions
Helper Functions
Predict
Helper functions for GP
Output
On-the-Fly Training
DFT Interface
Quantum Espresso
CP2K
VASP
Mapped Gaussian Process
Splines Methods
ASE Interface
FLARE ASE Calculator
On-the-fly training
GP From AIMD
Seed frames
Utility
Conversion between atomic numbers and element symbols
Conditions to add training data
Advanced Hyperparameters Set Up
Construct Atomic Environment
Utilities for Molecular Dynamics
I/O for trajectories
C++ Extension
Frequently Asked Questions
Frequently Asked Questions
Installation and Packages
Gaussian Processes and OTF
GPFA
MGP
Applications
How To Contribute
Git Workflow
General workflow
Master, development, and topic branches
Pushing changes to the MIR repo directly
Pushing changes from a forked repo
Code Standards
PEP 8
Docstrings
Tests
How to Cite
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